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comparison trinity.xml @ 2:1317615eff73 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3c4a2b13b0f3a280de4f98f4f5e0dc29e10fc7a0
author iuc
date Tue, 29 Mar 2016 06:46:09 -0400
parents fd94a21c2131
children 8ffafd84a7b8
comparison
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1:fd94a21c2131 2:1317615eff73
1 <tool id="trinity" name="Trinity" version="2.0.6.1"> 1 <tool id="trinity" name="Trinity" version="2.1.1">
2 <description>de novo assembly of RNA-Seq data</description> 2 <description>de novo assembly of RNA-Seq data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.0.6">trinity</requirement> 4 <requirement type="package" version="2.1.1">trinity</requirement>
5 <requirement type="package" version="1.1.2">bowtie</requirement> 5 <requirement type="package" version="1.1.2">bowtie</requirement>
6 <requirement type="package" version="1.2">samtools</requirement> 6 <requirement type="package" version="1.2">samtools</requirement>
7 <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement> 7 <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement>
8 </requirements> 8 </requirements>
9 <command><![CDATA[ 9 <command><![CDATA[
60 #end if 60 #end if
61 61
62 #end if 62 #end if
63 63
64 ## CPU and butterfly options. 64 ## CPU and butterfly options.
65 --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS} --bfly_opts "-V 10 --stderr" 65 --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr"
66 66
67 > $trinity_log 2>&1 67 ## > $trinity_log 2>&1
68 68
69 ]]></command> 69 ]]></command>
70 <inputs> 70 <inputs>
71 <conditional name="inputs"> 71 <conditional name="inputs">
72 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> 72 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
85 <option value="FR">Forward-Reverse</option> 85 <option value="FR">Forward-Reverse</option>
86 <option value="RF">Reverse-Forward</option> 86 <option value="RF">Reverse-Forward</option>
87 </param> 87 </param>
88 </when> 88 </when>
89 </conditional> 89 </conditional>
90 <param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/>
91 <param name="jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="set if you expect high gene density with UTR overlap"/> 90 <param name="jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="set if you expect high gene density with UTR overlap"/>
92 </when> 91 </when>
93 <when value="single"> 92 <when value="single">
94 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> 93 <param format="fasta,fastqsanger" name="input" type="data" label="Single-end reads" help=""/>
95 <conditional name="strand"> 94 <conditional name="strand">
96 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 95 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
97 <when value="false"> 96 <when value="false">
98 </when> 97 </when>
99 <when value="true"> 98 <when value="true">
128 127
129 <param format="fasta" name="long_reads" type="data" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/> 128 <param format="fasta" name="long_reads" type="data" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
130 </section> 129 </section>
131 </inputs> 130 </inputs>
132 <outputs> 131 <outputs>
133 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /> 132 <!--data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /-->
134 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> 133 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
135 </outputs> 134 </outputs>
136 <tests> 135 <tests>
137 <test> 136 <test>
138 <param name="paired_or_single" value="paired"/> 137 <param name="paired_or_single" value="paired"/>